A molecular orbital study of the conformation of formycin

Semiempirical quantum mechanical calculations, using the iterative extended Huckel theory, are carried out for the evaluation of conformational energies, dipole moment and net atomic charges as a function of the rotation about the glycosidic bond. Torsion about the C(4′)-C(5′) bond has also been considered. The energy diagrams for either the gg or gt rotamers of formycin predict that neither the first or the second energy minimum fall in the classical anti or syn regions. The predicted energy difference between the two most preferred conformations is rather large (3 kcal/mole). In contrast adenosine is predicted to favor the anti conformation by less than 1 kcal/mole. Barriers to internal counter-clockwise rotation about the glycosidic bond are higher for adenosine.     

A molecular orbital study of the conformation of barbiturates

The all-valence electrons molecular orbital method PCILO (Perturbative Configuration Interaction using Localized Orbitals) is applied to the study of the conformational and electronic properties of barbiturates. The results indicate the preference for specific conformations which correspond to a tendency for at least a partial folding of the aliphatic substituents towards the barbituric ring, and the eclipsing by the cyclic substituents of the bonds ending at C₅. The theoretical results agree with available experimental data from X-ray crystallography. On the other hand, the substituents at C₅ exert a negligible influence on the charge distribution in the barbituric ring. This situation agrees with the hypothesis that the factors responsible for the pharmacological activity of these drugs reside probably essentially in the electronic properties of the barbituric ring system (perhaps in its ability to hydrogen-bond with adenine), the role of the substituents at C₅ being mainly to favor the transfer of the drug to its receptors and the establishment of an appropriate contact with it.     

A molecular orbital study on the enzymic reaction mechanism of alpha-chymotrypsin

On the basis of the three-dimensional structure of the active site of α-chymotrypsin determined by X-ray diffraction analysis, we calculated a total energy and delocalization energy by using a molecular orbital method including all valence electrons, i.e. σ- and π-electrons. The calculated potential curve for a hydrolysis by a-chymotrypsin reproduced the experimental curve well, and the relative magnitudes of all steps in the reaction path explain the experimentally obtained activation energies satisfactorily. The validity of the “charge relay system” proposed by Blow and co-workers was investigated from the quantum-chemical point of view, and the possible importance of this structure for the acceleration of the hydrolysis through a proton transfer within the active site was pointed out. Delocalization energy was proved to play an important role in lowering the activation energy, and the effect of “orbital steering” suggested by Koshland and co-workers was also shown to be of importance for the catalytic reaction of α-chymotrypsin.     

A molecular mechanics and semiempirical molecular orbital study on the conformation of polynorbornene chains

The conformational analysis of polynorbornene (PNB) chains was investigated with the AM1, MM2, AMBER and OPLS methods taking into consideration the possibility of binding of norbornene monomers to each other at various positions, i.e. exo–exo, exo–endo, endo–endo. The chain that is formed by connecting exo–endo positions of the monomers has lower torsional barrier energy than those formed with bonds at other positions and has more flexibility. It is determined that the thredisyndiotactic chain formed by exo–endo addition adopts a helix structure and has a coil shape. The disyndiotactic chain formed by connecting norbornene monomers in mixed type has a linear structure. It is found that the repeat unit conformations of thredisyndiotactic and disyndiotactic chains of PNB are TGTG^– and (TGTG^–)₂, respectively.     

A molecular dynamics study on intermediate structures during transition from amorphous to crystalline state

Molecular dynamics (MD) simulations are carried out for model aluminium with 500, 864, 1372 and 2048 atoms interacting with Sutton-Chen version of embedded atom method (SCEAM) based on many body interactions. The systems equilibrated in an FCC structure have, first, been melted and then solidified with specifically selected single cooling rate which forms unstable amorphous state in the system. The local structures of the system have been analysed by bond orientational order parameters to distinguish the simple structures in the systems. The radial distribution functions (RDF) and atomic coordinates have also been analysed for determining the local structural properties. It has been observed that the phase sequences of the systems, except for those of the 2048 atoms, are FCC → Liquid → Amorphous → Mixed Crystal. Types of the crystals in the mixed state depend on the number of the atoms in the system. The final phase of the system with 2048 atoms is amorphous state.     

A molecular orbital study of stability and the conformation of double-stranded DNA-like polymers

The stacking and hydrogen bonding energies between bases in the B form of DNA were calculated by a perturbation method using the wave functions by the CNDO and the P-P-P methods. The exchange energies were calculated by using the corresponding orbitals. The magnitudes of the sums of the average stacking and hydrogen bonding energies per base pair of double-stranded DNA-like polymers are in good parallel with the melting temperatures of the polymers. The polymers containing I-C pairs are exceptions to this relation. Intrastrand stacking bases have the potential minimum at the distances of 2·8–3·7 Å. The minimum of stacking energy of double-stranded polymer for rotation of base pair around the helix axis exists near 36°. The deviation of the potential minimum from 36° seems to parallel the feature of the X-ray diffraction pattern of the polymer.     

Comparison of the mutagenic activity of the benzene metabolites, hydroquinone and para-benzoquinone in the supF forward mutation assay: a role for minor DNA adducts formed from hydroquinone in benzene mutagenicity

Benzene, a ubiquitous environmental pollutant and occupational hazardous chemical, is a recognised human leukaemogen and rodent carcinogen. The mechanism by which benzene exerts its carcinogenic effects is to date unknown but it is considered that mutations induced by benzene-DNA adducts may play a role. The benzene metabolite, para-benzoquinone (p-BQ) following reaction in vitro with DNA, forms four major adducts, which include two adducts on 2'-deoxyguanosine 3'-monophosphate (dGp). Reaction of DNA with the benzene metabolite hydroquinone (HQ) results in only one major DNA adduct, which corresponds to one of the dGp adducts formed following reaction with p-BQ. The mutagenicity of the adducts formed from these two benzene metabolites was investigated using the supF forward mutation assay. Metabolite-treated plasmid (pSP189) containing the supF gene was replicated in human Ad293 cells before being screened in indicator bacteria. Treatment with 5-20 mM p-BQ gave a 12 to 40-fold increase in mutation rate compared to 5-20 mM HQ treatment, a result reflected in the level of DNA modification observed (8 to 26-fold increase compared to HQ treatment). Treatment with p-BQ gave equal numbers of GC --> TA transversions and GC --> AT transitions, whereas treatment with HQ gave predominantly GC-->AT transitions. The spectra of mutations achieved for the two individual treatments were shown to be significantly different (P = 0.004). A combination of both treatments also resulted in a high level of GC --> AT transitions and a synergistic increase in the number of multiple mutations, which again predominated as GC --> AT transitions. Sites of mutational hotspots were observed for both individual treatments and one mutational hotspot was observed in the multiple mutations for the combined treatment. These results suggest that the dGp adducts formed from benzene metabolite treatment may play an important role in the mutagenicity and myelotoxicity of benzene.     

A molecular orbital study of the protein-controlled bathochromic shift in a model of rhodopsin

A molecular orbital study based on the Pariser-Parr-Pople method has been made of the effect of a negative charge on the long wavelength band of the protonated Schiff base of methylamine and retinal. The results show that the energy of the lowest transition, but not the oscillator strength, is highly dependent on the position of the negative charge. With the charge at infinity, the spectral maximum is found to be 524.7 nm. When the charge is moved closer to the Schiff base, the spectrum shows a blue shift from this value toward 440 nm. However, a red shift to about 556 nm is calculated when the charge is moved to the opposite end of the molecule. These results support the theories which hold that the position of a negative charge on the protein controls the observed spectral shifts on rhodopsin formation.     

Palmitoyl-L-carnitine, a metabolic intermediate of the fatty acid incorporation pathway in erythrocyte membrane phospholipids

In this paper we report that palmitoyl-L-carnitine can be a metabolic intermediate of the fatty acid incorporation pathway into erythrocyte membrane phosphatidylcholine, and phosphatidylethanolamine. Phospholipid acylation was evaluated by measuring the incorporation of radioactive [1-14C]-palmitoyl-L-carnitine in membrane erythrocyte ghost phospholipids in the presence or absence of CoA. CoA highly stimulated the incorporation of [1-14C]-palmitic acid into both the phospholipids examined, although the incorporation was also evident in the absence of added CoA. Incorporation of [1-14C]-palmitic acid into phosphatidylcholine was greater than into phosphatidylethanolamine. 2-Bromo-palmitoyl-CoA, an irreversible inhibitor of the erythrocyte carnitine palmitoyltransferase, inhibited the acylation process.     

A molecular orbital study on the oxidation of hydrogen donor molecules by peroxidase compound II

The electronic characteristics of some hydrogen donor substrate (phenol and aniline derivatives) for peroxidase reaction were calculated with the aid of the CNDO/2 and other methods. These results were compared with the experimental data concerning the rate of oxidation of these compounds by peroxidase and hydrogen peroxide. No simple relationship between the total or frontier electron densities on the oxygen or nitrogen atoms, or the lowest unoccupied orbital energies, and the rate of oxidation was found. It was, however, found that the logarithm of the rate of oxidation for the compounds studied correlates linearly with the highest occupied orbital energies. Based on these results, the mechanism of electron transfer from the substrate to compound II is discussed.     

Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems

The elucidation of organism-scale metabolic networks necessitates the development of integrative methods to analyze and interpret the systemic properties of cellular metabolism. A shift in emphasis from single metabolic reactions to systemically defined pathways is one consequence of such an integrative analysis of metabolic systems. The constraints of systemic stoichiometry, and limited thermodynamics have led to the definition of the flux space within the context of convex analysis. The flux space of the metabolic system, containing all allowable flux distributions, is constrained to a convex polyhedral cone in a high-dimensional space. From metabolic pathway analysis, the edges of the high-dimensional flux cone are vectors that correspond to systemically defined "extreme pathways" spanning the capabilities of the system. The addition of maximum flux capacities of individual metabolic reactions serves to further constrain the flux space and has led to the development of flux balance analysis using linear optimization to calculate optimal flux distributions. Here we provide the precise theoretical connections between pathway analysis and flux balance analysis allowing for their combined application to study integrated metabolic function. Shifts in metabolic behavior are calculated using linear optimization and are then interpreted using the extreme pathways to demonstrate the concept of pathway utilization. Changes to the reaction network, such as the removal of a reaction, can lead to the generation of suboptimal phenotypes that can be directly attributed to the loss of pathway function and capabilities. Optimal growth phenotypes are calculated as a function of environmental variables, such as the availability of substrate and oxygen, leading to the definition of phenotypic phase planes. It is illustrated how optimality properties of the computed flux distributions can be interpreted in terms of the extreme pathways. Together these developments are applied to an example network and to core metabolism of Escherichia coli demonstrating the connections between the extreme pathways, optimal flux distributions, and phenotypic phase planes. The consequences of changing environmental and internal conditions of the network are examined for growth on glucose and succinate in the face of a variety of gene deletions. The convergence of the calculation of optimal phenotypes through linear programming and the definition of extreme pathways establishes a different perspective for the understanding of how a defined metabolic network is best used under different environmental and internal conditions or, in other words, a pathway basis for the interpretation of the metabolic reaction norm.     

An explanation of the induction of mutations by 2-aminopurine from an ab initio molecular orbital study

The molecular mechanism of induction of mutations by 2-aminopurine (AP) was studied by an ab initio molecular orbital method. Cytosine (C) is converted to its disfavored imino tautomer more easily than AP, judging from the calculated total energies of the bases and the base analogue. This suggests that a stable AP:C base mispair via two hydrogen bonds can be formed with the imino tautomer of C. These results stress the importance of the imino form of C in AP-induced mutagenesis and support the 'trigger mechanism', in which formation of one hydrogen bond between AP and C is considered to stimulate the tautomeric shift of AP or C. The calculated relative stabilities of various base pairs and mispairs were in good agreement with experimental findings.     

An ab initio molecular orbital study on the characteristics of 8-hydroxyguanine

To investigate the mechanism by which the 8-hydroxyguanine residue in DNA affects the fidelity of DNA replication, the intrinsic properties of this modified base were investigated using an ab initio molecular orbital method. The most stable 8-hydroxyguanine form was revealed to be 6,8-diketo. The addition of an oxygen atom to the 8 position of a guanine base was shown to change the electrostatic potential of the molecule entirely and to give it a negative character. This effect may influence the local structure of 8-hydroxyguanine-containing DNA and the interaction with DNA polymerase, thereby resulting in infidelity of DNA replication.     

A molecular orbital study of the reaction catalysed by the enzyme adenosine kinase and its active site

The electronic characteristics of some adenine analogues were calculated with the aid of the semi-empirical SCF MO method of Pariser &; Parr (1953) and Pople (1953). These results were compared with the experimental data concerning the substrate specificity of adenosine kinase. No simple relation between the Michaelis constants and pi-electronic characteristics of the base moieties was found. It was found, however, that the logarithms of phosphorylation rates for the studied riboside analogues of adenosine correlate linearly with the electronic indices calculated for N₃ of the corresponding base moiety. This relation, in addition to the available enzymological data, suggests that adenosine forms a chelate complex with the cofactor Mg²⁺ (or other Me²⁺) being in syn-conformation. A tentative structure of the enzyme-substrate complex is considered on the basis of a possible mode of binding of this chelate to adenosine kinase.     

Identification of phyllostine as an intermediate of the patulin pathway in Penicillium urticae.

A patulin negative mutant (J1) of Penicillium urticae (NRRL 2159A) was found to accumulate large quantities (greater than 128 mg/L culture) of a reactive, photosensitive compound, which was isolated and identified as (-)-phyllostine (5,6-epoxygentisylquinone). This epoxyquinone possessed an antibiotic activity against Bacillus subtilis which was approximately 80% of that exhibited by patulin. In separate in vivo feeding experiments, [2-14C]acetate and [G-3H]gentisaldehyde were readily incorporated into phyllostine by mutant J1 and [14C]phyllostine was incorporated into patulin by the parent strain (NRRL 2159A). When fed to a washed-cell suspension of a second patulin negative mutant (J2) which produced gentisaldehyde but not phyllostine, unlabeled phyllostine was efficiently converted to patulin in yields of 33, 56, and 92% after 30 min, 1 and 5 h, respectively. The role of phyllostine as an intermediate of a new post-gentisaldehyde portion of the patulin biosynthetic pathway is discussed.